RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM

RAxML-NG was called at 12-Jul-2021 18:15:36 as follows:

raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/2_msa/Q9Y3A0_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/3_mltree/Q9Y3A0.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0 --threads 4

Analysis options:
  run mode: Ancestral state reconstruction
  start tree(s): user
  random seed: 1626102936
  tip-inner: ON
  pattern compression: OFF
  per-rate scalers: OFF
  site repeats: OFF
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/2_msa/Q9Y3A0_nogap_msa.fasta
[00:00:00] Loaded alignment with 958 taxa and 265 sites

WARNING: Sequences tr_A0A1B6PP26_A0A1B6PP26_SORBI_4558 and tr_A0A2T7D1N5_A0A2T7D1N5_9POAL_1504633 are exactly identical!
WARNING: Sequences sp_Q1EAH9_COQ4_COCIM_246410 and tr_A0A0J6XVT3_A0A0J6XVT3_COCIT_404692 are exactly identical!
WARNING: Sequences sp_B8NV05_COQ4_ASPFN_332952 and sp_Q2U523_COQ4_ASPOR_510516 are exactly identical!
WARNING: Sequences sp_B8NV05_COQ4_ASPFN_332952 and tr_A0A1S9DIB3_A0A1S9DIB3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_F9G175_F9G175_FUSOF_660025 and tr_N4UI88_N4UI88_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G175_F9G175_FUSOF_660025 and tr_A0A2H3TEM4_A0A2H3TEM4_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9G175_F9G175_FUSOF_660025 and tr_A0A2K0VZ52_A0A2K0VZ52_GIBNY_42673 are exactly identical!
WARNING: Sequences sp_A5ABP2_COQ4_ASPNC_425011 and tr_G3YBP8_G3YBP8_ASPNA_380704 are exactly identical!
WARNING: Sequences sp_A5ABP2_COQ4_ASPNC_425011 and tr_A0A319BEW7_A0A319BEW7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XFD1_G7XFD1_ASPKW_1033177 and tr_A0A100IPJ2_A0A100IPJ2_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XFD1_G7XFD1_ASPKW_1033177 and tr_A0A146FSL5_A0A146FSL5_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XFD1_G7XFD1_ASPKW_1033177 and tr_A0A1L9N233_A0A1L9N233_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_G7XFD1_G7XFD1_ASPKW_1033177 and tr_A0A317UW65_A0A317UW65_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_I1PQU5_I1PQU5_ORYGL_4538 and tr_A0A0D3G1L8_A0A0D3G1L8_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1PQU5_I1PQU5_ORYGL_4538 and tr_A0A0D9ZSC7_A0A0D9ZSC7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_I1PQU5_I1PQU5_ORYGL_4538 and tr_Q7XQ99_Q7XQ99_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0D2XI39_A0A0D2XI39_FUSO4_426428 and tr_A0A2H3GS23_A0A2H3GS23_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_W2PH25_W2PH25_PHYPN_761204 and tr_A0A0W8D295_A0A0W8D295_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_A0A015LAH1_A0A015LAH1_9GLOM_1432141 and tr_A0A2H5S1G9_A0A2H5S1G9_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A094EJV0_A0A094EJV0_9PEZI_1420912 and tr_A0A1B8GTZ9_A0A1B8GTZ9_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0F8UG82_A0A0F8UG82_9EURO_308745 and tr_A0A2T5M068_A0A2T5M068_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0G4P1H3_A0A0G4P1H3_PENCA_1429867 and tr_A0A124GT53_A0A124GT53_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0V0WEQ9_A0A0V0WEQ9_9BILA_92179 and tr_A0A0V0TM41_A0A0V0TM41_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1Q3DWM8_A0A1Q3DWM8_LENED_5353 and tr_A0A1Q3DX41_A0A1Q3DX41_LENED_5353 are exactly identical!
WARNING: Sequences tr_A0A1U8EX28_A0A1U8EX28_CAPAN_4072 and tr_A0A2G3B6Y4_A0A2G3B6Y4_CAPCH_80379 are exactly identical!
WARNING: Duplicate sequences found: 25

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0.raxml.reduced.phy

Alignment comprises 1 partitions and 265 sites

Partition 0: noname
Model: LG4X+R4
Alignment sites: 265
Gaps: 14.55 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/3_mltree/Q9Y3A0.raxml.bestTree_unrooted
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 67 / 5360
[00:00:00] Data distribution: max. searches per worker: 1

Starting ML tree search with 1 distinct starting trees

[00:00:00] Tree #1, initial LogLikelihood: -128986.451799

[00:00:00 -128986.451799] Initial branch length optimization
[00:00:01 -128239.299237] Model parameter optimization (eps = 0.100000)

[00:00:37] Tree #1, final logLikelihood: -127769.088781


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.159325,0.286532) (0.235340,0.327468) (0.341516,0.888538) (0.263819,2.175099) 
   Base frequencies (model): 
M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 
M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 
M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 
M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 
   Substitution rates (model): 
M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 
M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 
M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 
M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 

Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0.raxml.ancestralProbs
Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0.raxml.ancestralStates
Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0.raxml.ancestralTree

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y3A0/4_raxmlng_ancestral/Q9Y3A0.raxml.log

Analysis started: 12-Jul-2021 18:15:36 / finished: 12-Jul-2021 18:16:16

Elapsed time: 40.023 seconds

Consumed energy: 2.552 Wh